May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cytb_40_cIV_B_40_human
Genes: A B A+B
Length: 378 227 598
Sequences: 3801 4297 1458
Seq/Len: 10.06 18.93 2.44
MirrorTree (Pazo et al. 2001) 0.74
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.01 0.12
2 0.02 0.01 0.19
5 0.02 0.01 0.55
10 0.02 0.01 1.70
20 0.02 0.01 1.80
100 0.02 0.02 1.91
∞ 0.03 0.07 2.41
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
37_L 205_S 1.22 0.80 0.06
322_Q 12_A 1.13 0.72 0.05
283_S 144_L 1.05 0.64 0.04
102_L 68_L 0.94 0.51 0.03
252_D 205_S 0.94 0.51 0.03
292_L 39_L 0.93 0.50 0.03
188_I 32_F 0.92 0.49 0.03
164_I 76_I 0.91 0.48 0.02
119_L 76_I 0.91 0.47 0.02
355_S 4_A 0.89 0.45 0.02
234_L 215_P 0.88 0.44 0.02
173_P 88_D 0.87 0.43 0.02
66_I 165_V 0.87 0.43 0.02
304_I 95_L 0.85 0.41 0.02
57_P 138_V 0.85 0.41 0.02
155_Y 35_C 0.85 0.41 0.02
121_L 41_A 0.85 0.40 0.02
316_M 32_F 0.83 0.39 0.02
364_I 36_F 0.82 0.38 0.02
140_F 14_S 0.81 0.37 0.02
343_V 97_I 0.81 0.36 0.02
211_I 43_F 0.81 0.36 0.02
55_Y 37_L 0.80 0.35 0.02
318_R 4_A 0.80 0.35 0.02
37_L 86_M 0.78 0.33 0.01
82_L 155_T 0.78 0.33 0.01
245_F 150_I 0.78 0.33 0.01
331_D 99_S 0.78 0.33 0.01
248_D 156_S 0.78 0.33 0.01
101_G 138_V 0.77 0.32 0.01
246_S 165_V 0.77 0.32 0.01
21_L 205_S 0.77 0.32 0.01
334_I 172_T 0.77 0.32 0.01
166_G 176_P 0.76 0.32 0.01
156_I 47_T 0.76 0.32 0.01
189_I 150_I 0.76 0.31 0.01
47_T 9_L 0.76 0.31 0.01
23_T 16_I 0.76 0.31 0.01
313_Q 23_F 0.75 0.30 0.01
179_F 38_V 0.75 0.30 0.01
297_S 22_T 0.75 0.30 0.01
193_A 110_Y 0.75 0.30 0.01
46_T 165_V 0.75 0.30 0.01
353_V 192_Y 0.74 0.29 0.01
308_H 8_G 0.74 0.29 0.01
242_L 123_L 0.74 0.29 0.01
94_L 184_F 0.74 0.29 0.01
55_Y 107_T 0.74 0.29 0.01
173_P 67_I 0.74 0.29 0.01
230_L 185_T 0.74 0.29 0.01
261_P 67_I 0.74 0.29 0.01
238_S 165_V 0.73 0.28 0.01
292_L 210_V 0.73 0.28 0.01
274_F 162_S 0.72 0.28 0.01
42_I 92_D 0.72 0.27 0.01
355_S 30_I 0.72 0.27 0.01
69_I 63_T 0.72 0.27 0.01
58_D 13_T 0.72 0.27 0.01
254_D 28_L 0.71 0.27 0.01
345_Y 192_Y 0.71 0.27 0.01
340_G 58_A 0.71 0.26 0.01
223_Y 155_T 0.71 0.26 0.01
129_M 3_H 0.71 0.26 0.01
98_I 68_L 0.71 0.26 0.01
353_V 126_L 0.71 0.26 0.01
158_T 152_M 0.70 0.26 0.01
238_S 123_L 0.70 0.26 0.01
45_I 155_T 0.70 0.26 0.01
242_L 34_I 0.70 0.26 0.01
105_G 214_I 0.70 0.26 0.01
221_H 175_I 0.70 0.25 0.01
99_G 119_N 0.70 0.25 0.01
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
5399 2.44 cytb_40_cIV_B_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.04 Done - Shared
5398 2.44 cytb_40_cIV_B_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.12 Done - Shared
5397 2.45 cytb_20_cIV_B_40_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.03 Done - Shared
5396 1.92 cytb_80_cIV_B_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.03 Done - Shared
5395 2.44 cytb_40_cIV_B_40_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.06 Done - Shared
5392 2.44 cytb_40_cIV_B_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.07 Done - Shared
Page generated in 0.5467 seconds.